3MFI

DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JIHPDB ENTRY 1JIH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.527733% PEG 4000, 0.1 M TRIS, 0.2 M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2261.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.087α = 90
b = 226.962β = 90
c = 85.919γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.0809APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.765099.80.12910.57.28568985518
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.761.8299.60.6656.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1JIH1.76358573281185427399.680.164750.163540.18721RANDOM21.038
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.23-0.310.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.678
r_dihedral_angle_4_deg20.581
r_dihedral_angle_3_deg12.731
r_dihedral_angle_1_deg5.862
r_scangle_it3.315
r_scbond_it2.106
r_angle_refined_deg1.59
r_mcangle_it1.39
r_angle_other_deg0.902
r_mcbond_it0.714
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.678
r_dihedral_angle_4_deg20.581
r_dihedral_angle_3_deg12.731
r_dihedral_angle_1_deg5.862
r_scangle_it3.315
r_scbond_it2.106
r_angle_refined_deg1.59
r_mcangle_it1.39
r_angle_other_deg0.902
r_mcbond_it0.714
r_mcbond_other0.178
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4035
Nucleic Acid Atoms508
Solvent Atoms709
Heterogen Atoms42

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
PHASERphasing